The much-hyped running style that had weekend warriors ditching sneakers to jog with little or nothing on their feet, as humans had for millennia before the advent of footwear, is falling out of favor.

Health claims that had helped drive the trend are coming under attack. Vibram, which makes the FiveFingers shoes that look like gloves for the feet, has offered to settle a class-action suit that contends the company profited from unsubstantiated claims the shoes strengthen muscles and prevent injury.

Vibram has proposed to reimburse buyers up to $94 for every pair they have purchased. The proposed settlement is awaiting approval from a U.S. district court in Massachusetts.

Meanwhile, sales of so-called minimalist shoes with ultra-thin soles have plunged 47% so far this year, even as total running-shoe sales have risen slightly. Last year, minimalist footwear was the only major category to shrink, dropping by a third to $220 million, while the running-shoe market as a whole grew slightly to $7 billion, according to data from industry tracker SportsOneSource.

That is a swift reversal for a type of shoe that had been leading growth in running footwear. Sales of minimalist footwear were the fastest-growing segment in running in the first two years of this decade, and in 2011 alone had nearly quintupled to about $157 million from the year before.

As the fad took off, shoe manufacturers churned out new models without any cushioning to get as close to barefoot running as possible while still protecting feet from 21st-century hazards like glass and asphalt.

One reason for the downturn, experts say, is that the fad was pitched as a panacea for common injuries from knee pain to shin splints. But the results didn’t meet expectations. Runners instead found themselves with a new set of complaints including blisters and calf pain.

Sharon Gibson, a personal trainer in Ferndale, Mich., bought a pair of ultraminimalist Vibram FiveFingers shoes in 2012. After reading several books on barefoot running—especially the 2009 best seller “Born to Run” —she became enamored of the idea that chucking her heavy, traditional shoes wouldn’t just be liberating, but better for her.

“I liked the science they were bringing out, the idea that it was healthier for your foot,” she said.

But Ms. Gibson, 46 years old, said she had a hard time adjusting to the Vibrams, which cost her more than $100. She could wear them only for about half a mile before her calves began to ache, and she didn’t want to risk injury while training for a marathon. After a month, she was back to running in more traditional shoes full time.

The backlash against barefoot-style shoes is bringing in “maximal” shoes made with plush cushioning. Models made by Deckers Outdoor Corp.’s DECK +3.79% Hoka One One are already best sellers at Colorado-based chain Boulder Running Co, said Mark Plaatjes, the specialty stores’ co-founder.

Not all minimalist models are expiring, especially the ones that are evolving. The NikeNKE +0.55% Free, introduced in 2004 and considered the first mass-market ultrathin-soled shoe, is excluded from the minimalist sales totals compiled by SportsOneSource, because the shoe—which looks like a traditional sneaker—appeals as much to the fashionable as the athletic, analyst Matt Powell said.

Even Vibram is adjusting. The closely held company introduced a new, more cushioned version of its FiveFingers glovelike shoes this spring in response to consumers who have lost faith in the barefoot way.

Vibram USA Chief Executive Mike Gionfriddo said the company is always appreciative of consumer feedback, and that its shoes “are a matter of personal preference.”

Adidas AG continues to make a split-toed training shoe, the AdiPure Trainer 1.1, which was designed for use in the gym, according to spokeswoman Lauren Lamkin. Sales for the company’s minimalist running line are “small and about the same as it was before the fad,” Ms. Lamkin said.

Among academics, the jury is still out on whether footwear choice, of any type, has an impact on injury rates.

“Public discussion got way ahead of science,” said Dan Lieberman, a professor of human evolutionary biology at Harvard, whose research on running form was featured in “Born to Run,” which was written by Christopher McDougall and largely credited for popularizing the trend.

Mr. Lieberman also served as a consultant to Vibram, according to documents in the Vibram case. Mr. Lieberman disputes that he was a consultant for the company, but said Vibram gave a gift to Harvard’s lab to fund research on barefoot running, adding that the lab didn’t test Vibram shoes.

Mr. McDougall said he doesn’t regret the impact his work has had on the minimalist boom, but it was never his intention at the time.

John Durant, a self-described “professional caveman” in New York City and founder of the meet-up group Barefoot Runners NYC, said he started doing many of his runs totally shoeless some five years ago, but has noticed a backlash has developed against so-called gorilla shoes with toes.